151
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Giamblanco N, Conoci S, Russo D, Marletta G. Single-step label-free hepatitis B virus detection by a piezoelectric biosensor. RSC Adv 2015. [DOI: 10.1039/c5ra03467a] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Probe densityvs.genome recognition selectivity.
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Affiliation(s)
- Nicoletta Giamblanco
- Laboratory for Molecular Surfaces and Nanotechnology (LAMSUN)
- Department of Chemical Sciences
- University of Catania and CSGI
- 95125 Catania
- Italy
| | | | | | - Giovanni Marletta
- Laboratory for Molecular Surfaces and Nanotechnology (LAMSUN)
- Department of Chemical Sciences
- University of Catania and CSGI
- 95125 Catania
- Italy
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152
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Gates EP, Jensen JK, Harb JN, Woolley AT. Optimizing gold nanoparticle seeding density on DNA origami. RSC Adv 2015. [DOI: 10.1039/c4ra15451g] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Characterization of various experimental parameters leads to optimized conditions for depositing linear strings of gold nanoparticle seeds on DNA origami.
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Affiliation(s)
- E. P. Gates
- Department of Chemistry and Biochemistry
- Brigham Young University
- Provo
- USA
| | - J. K. Jensen
- Department of Chemistry and Biochemistry
- Brigham Young University
- Provo
- USA
| | - J. N. Harb
- Department of Chemical Engineering
- Brigham Young University
- Provo
- USA
| | - A. T. Woolley
- Department of Chemistry and Biochemistry
- Brigham Young University
- Provo
- USA
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153
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Abstract
The DNA origami method enables the creation of complex nanoscale objects that can be used to organize molecular components and to function as reconfigurable mechanical devices. Of relevance to synthetic biology, DNA origami structures can be delivered to cells where they can perform complicated sense-and-act tasks, and can be used as scaffolds to organize enzymes for enhanced synthesis. The design of DNA origami structures is a complicated matter and is most efficiently done using dedicated software packages. This chapter describes a procedure for designing DNA origami structures using a combination of state-of-the-art software tools. First, we introduce the basic method for calculating crossover positions between DNA helices and the standard crossover patterns for flat, square, and honeycomb DNA origami lattices. Second, we provide a step-by-step tutorial for the design of a simple DNA origami biosensor device, from schematic idea to blueprint creation and to 3D modeling and animation, and explain how careful modeling can facilitate later experimentation in the laboratory.
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Affiliation(s)
- Denis Selnihhin
- Center for DNA Nanotechnology, Interdisciplinary Nanoscience Center, Department of Molecular Biology & Genetics, Aarhus University, 8000, Aarhus, Denmark
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154
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Wang L, Arrabito G. Hybrid, multiplexed, functional DNA nanotechnology for bioanalysis. Analyst 2015; 140:5821-48. [DOI: 10.1039/c5an00861a] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
DNA nanotechnology allows for the realization of novel multiplexed assays in bioanalytical sciences.
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Affiliation(s)
- L. Wang
- Department of Chemical Science and Technologies & NAST Center
- University of Rome Tor Vergata
- 00133 Rome
- Italy
| | - G. Arrabito
- Department of Electronic Engineering
- University of Rome Tor Vergata
- Rome
- Italy
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155
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Ma C, Wu Z, Wang W, Jiang Q, Shi C. Three-dimensional DNA nanostructures for colorimetric assay of nucleic acids. J Mater Chem B 2015; 3:2853-2857. [DOI: 10.1039/c4tb02049a] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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156
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Lan X, Lu X, Shen C, Ke Y, Ni W, Wang Q. Au Nanorod Helical Superstructures with Designed Chirality. J Am Chem Soc 2014; 137:457-62. [DOI: 10.1021/ja511333q] [Citation(s) in RCA: 232] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Xiang Lan
- Key
Laboratory of Nano-Bio Interface, Division of Nanobiomedicine and
i-Lab, CAS Center for Excellence in Brain Science, Suzhou Institute
of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123 China
| | - Xuxing Lu
- Key
Laboratory of Nano-Bio Interface, Division of Nanobiomedicine and
i-Lab, CAS Center for Excellence in Brain Science, Suzhou Institute
of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123 China
| | - Chenqi Shen
- Key
Laboratory of Nano-Bio Interface, Division of Nanobiomedicine and
i-Lab, CAS Center for Excellence in Brain Science, Suzhou Institute
of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123 China
| | - Yonggang Ke
- Wallace
H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - Weihai Ni
- Key
Laboratory of Nano-Bio Interface, Division of Nanobiomedicine and
i-Lab, CAS Center for Excellence in Brain Science, Suzhou Institute
of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123 China
| | - Qiangbin Wang
- Key
Laboratory of Nano-Bio Interface, Division of Nanobiomedicine and
i-Lab, CAS Center for Excellence in Brain Science, Suzhou Institute
of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123 China
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157
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Setyawati MI, Kutty RV, Tay CY, Yuan X, Xie J, Leong DT. Novel theranostic DNA nanoscaffolds for the simultaneous detection and killing of Escherichia coli and Staphylococcus aureus. ACS APPLIED MATERIALS & INTERFACES 2014; 6:21822-31. [PMID: 24941440 DOI: 10.1021/am502591c] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
A novel theranostic platform is made by utilizing a self-assembled DNA nanopyramid (DP) as scaffold for incorporation of both detection and therapeutic moieties to combat bacterial infection. Red-emissive glutathione-protected gold nanoclusters (GSH-Au NCs) were used for bacterial detection. Actinomycin D (AMD) that was intercalated on the DP scaffold was used as therapeutic agent. This results in the formation of theranostic DPAu/AMD. Model bacteria Escherichia coli and Staphylococcus aureus were found to be readily taken in the DPAu/AMD and be susceptible to its killing effect. In addition, DPAu/AMD was observed to outperform the free AMD in killing infectious bacteria. The degradation of the DP structure by DNase was found to be responsible for the release of AMD and the effective killing effect of the infectious bacteria. This novel strategy presents a basic platform for future improvements to detect infectious bacteria and treatment.
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Affiliation(s)
- Magdiel I Setyawati
- Department of Chemical and Biomolecular Engineering, National University of Singapore , 4 Engineering 4, Singapore 117585, Singapore
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158
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Yan J, Hu C, Wang P, Liu R, Zuo X, Liu X, Song S, Fan C, He D, Sun G. Novel rolling circle amplification and DNA origami-based DNA belt-involved signal amplification assay for highly sensitive detection of prostate-specific antigen (PSA). ACS APPLIED MATERIALS & INTERFACES 2014; 6:20372-20377. [PMID: 25323204 DOI: 10.1021/am505913d] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Prostate-specific antigen (PSA) is one of the most important biomarkers for the early diagnosis and prognosis of prostate cancer. Although many efforts have been made to achieve significant progress for the detection of PSA, challenges including relative low sensitivity, complicated operation, sophisticated instruments, and high cost remain unsolved. Here, we have developed a strategy combining rolling circle amplification (RCA)-based DNA belts and magnetic bead-based enzyme-linked immunosorbent assay (ELISA) for the highly sensitive and specific detection of PSA. At first, a 96-base circular DNA template was designed and prepared for the following RCA. Single stranded DNA (ssDNA) products from RCA were used as scaffold strand for DNA origami, which was hybridized with three staple strands of DNA. The resulting DNA belts were conjugated with multiple enzymes for signal amplification and then employed to magnetic bead based ELISA for PSA detection. Through our strategy, as low as 50 aM of PSA can be detected with excellent specificity.
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Affiliation(s)
- Juan Yan
- Department of Medical Imaging, Jinan Military General Hospital , Shandong Province 250031, China
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159
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160
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Olejko L, Cywinski PJ, Bald I. Ion-Selective Formation of a Guanine Quadruplex on DNA Origami Structures. Angew Chem Int Ed Engl 2014; 54:673-7. [DOI: 10.1002/anie.201409278] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Indexed: 01/14/2023]
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161
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Hernández-Ainsa S, Keyser UF. DNA origami nanopores: developments, challenges and perspectives. NANOSCALE 2014; 6:14121-32. [PMID: 25325422 DOI: 10.1039/c4nr04094e] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
DNA nanotechnology has enabled the construction of DNA origami nanopores; synthetic nanopores that present improved capabilities for the area of single molecule detection. Their extraordinary versatility makes them a new and powerful tool in nanobiotechnology for a wide range of important applications beyond molecular sensing. In this review, we briefly present the recent developments in this emerging field of research. We discuss the current challenges and possible solutions that would enhance the sensing capabilities of DNA origami nanopores. Finally, we anticipate novel avenues for future research and highlight a range of exciting ideas and applications that could be explored in the near future.
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162
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Chao J, Liu H, Su S, Wang L, Huang W, Fan C. Structural DNA nanotechnology for intelligent drug delivery. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2014; 10:4626-4635. [PMID: 24955859 DOI: 10.1002/smll.201401309] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 06/02/2014] [Indexed: 06/03/2023]
Abstract
Drug delivery carriers have been popularly employed to improve solubility, stability, and efficacy of chemical and biomolecular drugs. Despite the rapid progress in this field, it remains a great challenge to develop an ideal carrier with minimal cytotoxicity, high biocompatibility and intelligence for targeted controlled release. The emergence of DNA nanotechnology offers unprecedented opportunities in this regard. Due to the unparalleled self-recognition properties of DNA molecules, it is possible to create numerous artificial DNA nanostructures with well-defined structures and DNA nanodevices with precisely controlled motions. More importantly, recent studies have proven that DNA nanostructures possess greater permeability to the membrane barrier of cells, which pave the way to developing new drug delivery carriers with nucleic acids, are summarized. In this Concept, recent advances on the design and fabrication of both static and dynamic DNA nanostructures, and the use of these nanostructures for the delivery of various types of drugs, are highlighted. It is also demonstrated that dynamic DNA nanostructures provide the required intelligence to realize logically controlled drug release.
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Affiliation(s)
- Jie Chao
- Division of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China; Key Laboratory for Organic Electronics & Information Displays (KLOEID), Institute of Advanced Materials (IAM) and School of Materials Science and Engineering, Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing, 210046, China
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163
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Sun S, Yao H, Zhang F, Zhu J. Multiplexed DNA detection based on positional encoding/decoding with self-assembled DNA nanostructures. Chem Sci 2014; 6:930-934. [PMID: 29560179 PMCID: PMC5811145 DOI: 10.1039/c4sc02696a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 10/15/2014] [Indexed: 01/02/2023] Open
Abstract
A multiplexed DNA detection strategy with fast hybridization kinetics based on positional encoding/decoding with self-assembled DNA nanostructures has been developed.
Current multiplexed analysis methods suffer from either slow reaction kinetics (planar arrays) or complicated encoding/decoding procedures (suspension arrays). We report herein a multiplexed DNA detection strategy that addresses these issues, based on positional encoding/decoding with self-assembled DNA nanostructures. The strategy enables the acquisition of high-resolution, consistent, and quantitative assay results in a single round of a transmission electron microscopy imaging operation. Applications in polymerase chain reaction-free settings and assays of other structurally distinct targets can be anticipated through the implementation of the strategy with miniaturized femtoliter/attoliter dispensing technology and readily accessible DNA conjugate structures.
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Affiliation(s)
- Sha Sun
- Department of Polymer Science and Engineering , School of Chemistry and Chemical Engineering , State Key Laboratory of Coordination Chemistry , Nanjing National Laboratory of Microstructures , Nanjing University , Nanjing 210093 , China .
| | - Huaxin Yao
- Department of Polymer Science and Engineering , School of Chemistry and Chemical Engineering , State Key Laboratory of Coordination Chemistry , Nanjing National Laboratory of Microstructures , Nanjing University , Nanjing 210093 , China .
| | - Feifei Zhang
- Department of Polymer Science and Engineering , School of Chemistry and Chemical Engineering , State Key Laboratory of Coordination Chemistry , Nanjing National Laboratory of Microstructures , Nanjing University , Nanjing 210093 , China .
| | - Jin Zhu
- Department of Polymer Science and Engineering , School of Chemistry and Chemical Engineering , State Key Laboratory of Coordination Chemistry , Nanjing National Laboratory of Microstructures , Nanjing University , Nanjing 210093 , China .
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164
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Zhang C, Sun Q, Sheng K, Tan Q, Xu W. Adsorption-geometry induced transformation of self-assembled nanostructures of an aldehyde molecule on Cu(110). NANOSCALE 2014; 6:11062-11065. [PMID: 25145767 DOI: 10.1039/c4nr03754e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
From an interplay of high-resolution STM imaging/manipulation and DFT calculations, we have revealed that different self-assembled nanostructures of BA molecules on Cu(110) are attributable to specific molecular adsorption geometries, and thus the corresponding intermolecular hydrogen bonding patterns. The STM manipulations demonstrate the feasibility of switching such weak-hydrogen-bonding patterns.
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Affiliation(s)
- Chi Zhang
- College of Materials Science and Engineering, Tongji University, Caoan Road 4800, Shanghai 201804, P. R. China.
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165
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Ye T, Chen J, Liu Y, Ji X, Zhou G, He Z. Periodic fluorescent silver clusters assembled by rolling circle amplification and their sensor application. ACS APPLIED MATERIALS & INTERFACES 2014; 6:16091-16096. [PMID: 25116051 DOI: 10.1021/am504035a] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
A simple method for preparing DNA-stabilized Ag nanoclusters (NCs) nanowires is presented. To fabricate the Ag NCs nanowires, we use just two unmodified component strands and a long enzymatically produced scaffold. These nanowires form at room temperature and have periodic sequence units that are available for fluorescence Ag NCs assembled which formed three-way junction (TWJ) structure. These Ag NCs nanowires can be clearly visualized by confocal microscopy. Furthermore, due to the high efficiency of rolling circle amplification reaction in signal amplification, the nanowires exhibit high sensitivity for the specific DNA detection with a wide linear range from 6 to 300 pM and a low detection limit of 0.84 pM, which shows good performance in the complex serum samples. Therefore, these Ag NCs nanowires might have great potential in clinical and imaging applications in the future.
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Affiliation(s)
- Tai Ye
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University , Wuhan 430072, P. R. China
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166
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Woo S, Rothemund PWK. Self-assembly of two-dimensional DNA origami lattices using cation-controlled surface diffusion. Nat Commun 2014; 5:4889. [PMID: 25205175 DOI: 10.1038/ncomms5889] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 08/01/2014] [Indexed: 12/24/2022] Open
Abstract
DNA origami has proven useful for organizing diverse nanoscale components into patterns with 6 nm resolution. However for many applications, such as nanoelectronics, large-scale organization of origami into periodic lattices is desired. Here, we report the self-assembly of DNA origami rectangles into two-dimensional lattices based on stepwise control of surface diffusion, implemented by changing the concentrations of cations on the surface. Previous studies of DNA–mica binding identified the fractional surface density of divalent cations (ñ(s2))as the parameter which best explains the behaviour of linear DNA on mica. We show that for ñ(s2) between 0.04 and 0.1, over 90% of DNA rectangles were incorporated into lattices and that, compared with other functions of cation concentration, ñ(s2) best captures the behaviour of DNA rectangles. This work shows how a physical understanding of DNA–mica binding can be used to guide studies of the higher-order assembly of DNA nanostructures, towards creating large-scale arrays of nanodevices for technology.
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Affiliation(s)
- Sungwook Woo
- Department of Bioengineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Paul W K Rothemund
- 1] Department of Bioengineering, California Institute of Technology, Pasadena, California 91125, USA [2] Department of Computer Science, California Institute of Technology, Pasadena, California 91125, USA [3] Department of Computation &Neural Systems, California Institute of Technology, Pasadena, California 91125, USA
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167
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Molecular processes studied at a single-molecule level using DNA origami nanostructures and atomic force microscopy. Molecules 2014; 19:13803-23. [PMID: 25191873 PMCID: PMC6271098 DOI: 10.3390/molecules190913803] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 08/21/2014] [Accepted: 08/29/2014] [Indexed: 12/26/2022] Open
Abstract
DNA origami nanostructures allow for the arrangement of different functionalities such as proteins, specific DNA structures, nanoparticles, and various chemical modifications with unprecedented precision. The arranged functional entities can be visualized by atomic force microscopy (AFM) which enables the study of molecular processes at a single-molecular level. Examples comprise the investigation of chemical reactions, electron-induced bond breaking, enzymatic binding and cleavage events, and conformational transitions in DNA. In this paper, we provide an overview of the advances achieved in the field of single-molecule investigations by applying atomic force microscopy to functionalized DNA origami substrates.
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168
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Zhang F, Nangreave J, Liu Y, Yan H. Structural DNA nanotechnology: state of the art and future perspective. J Am Chem Soc 2014; 136:11198-211. [PMID: 25029570 PMCID: PMC4140475 DOI: 10.1021/ja505101a] [Citation(s) in RCA: 393] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Indexed: 12/12/2022]
Abstract
Over the past three decades DNA has emerged as an exceptional molecular building block for nanoconstruction due to its predictable conformation and programmable intra- and intermolecular Watson-Crick base-pairing interactions. A variety of convenient design rules and reliable assembly methods have been developed to engineer DNA nanostructures of increasing complexity. The ability to create designer DNA architectures with accurate spatial control has allowed researchers to explore novel applications in many directions, such as directed material assembly, structural biology, biocatalysis, DNA computing, nanorobotics, disease diagnosis, and drug delivery. This Perspective discusses the state of the art in the field of structural DNA nanotechnology and presents some of the challenges and opportunities that exist in DNA-based molecular design and programming.
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Affiliation(s)
- Fei Zhang
- Center
for Molecular Design and Biomimicry, Biodesign Institute, and Department of
Chemistry and Biochemistry, Arizona State
University, Tempe, Arizona 85287, United
States
| | - Jeanette Nangreave
- Center
for Molecular Design and Biomimicry, Biodesign Institute, and Department of
Chemistry and Biochemistry, Arizona State
University, Tempe, Arizona 85287, United
States
| | - Yan Liu
- Center
for Molecular Design and Biomimicry, Biodesign Institute, and Department of
Chemistry and Biochemistry, Arizona State
University, Tempe, Arizona 85287, United
States
| | - Hao Yan
- Center
for Molecular Design and Biomimicry, Biodesign Institute, and Department of
Chemistry and Biochemistry, Arizona State
University, Tempe, Arizona 85287, United
States
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169
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Torelli E, Marini M, Palmano S, Piantanida L, Polano C, Scarpellini A, Lazzarino M, Firrao G. A DNA origami nanorobot controlled by nucleic acid hybridization. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2014; 10:2918-2926. [PMID: 24648163 DOI: 10.1002/smll.201400245] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 02/26/2014] [Indexed: 06/03/2023]
Abstract
A prototype for a DNA origami nanorobot is designed, produced, and tested. The cylindrical nanorobot (diameter of 14 nm and length of 48 nm) with a switchable flap, is able to respond to an external stimulus and reacts by a physical switch from a disarmed to an armed configuration able to deliver a cellular compatible message. In the tested design the robot weapon is a nucleic acid fully contained in the inner of the tube and linked to a single point of the internal face of the flap. Upon actuation the nanorobot moves the flap extracting the nucleic acid that assembles into a hemin/G-quadruplex horseradish peroxidase mimicking DNAzyme catalyzing a colorimetric reaction or chemiluminescence generation. The actuation switch is triggered by an external nucleic acid (target) that interacts with a complementary nucleic acid that is beard externally by the nanorobot (probe). Hybridization of probe and target produces a localized structural change that results in flap opening. The flap movement is studied on a two-dimensional prototype origami using Förster resonance energy transfer and is shown to be triggered by a variety of targets, including natural RNAs. The nanorobot has potential for in vivo biosensing and intelligent delivery of biological activators.
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Affiliation(s)
- Emanuela Torelli
- Department of Agricultural and Environmental Sciences, University of Udine, via delle Scienze 206, 33100, Udine, Italy
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170
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Lu X, Watts E, Jia F, Tan X, Zhang K. Polycondensation of Polymer Brushes via DNA Hybridization. J Am Chem Soc 2014; 136:10214-7. [DOI: 10.1021/ja504790r] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Xueguang Lu
- Department of Chemistry and
Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Eleanor Watts
- Department of Chemistry and
Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Fei Jia
- Department of Chemistry and
Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Xuyu Tan
- Department of Chemistry and
Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Ke Zhang
- Department of Chemistry and
Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
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171
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Tintoré M, Eritja R, Fábrega C. DNA Nanoarchitectures: Steps towards Biological Applications. Chembiochem 2014; 15:1374-90. [DOI: 10.1002/cbic.201402014] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Indexed: 12/26/2022]
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172
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Chen N, Li J, Song H, Chao J, Huang Q, Fan C. Physical and biochemical insights on DNA structures in artificial and living systems. Acc Chem Res 2014; 47:1720-30. [PMID: 24588263 DOI: 10.1021/ar400324n] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
CONSPECTUS: Highly specific DNA base-pairing is the basis for both fulfilling its genetic role and constructing novel nanostructures and hybrid conjugates with inorganic nanomaterials (NMs). There exist many remarkable differences in the physical properties of single-stranded (ss) and double-stranded (ds) DNA, which play important roles in regulation of biological processes in nature. Rapid advances in nanoscience and nanotechnology pose new questions on how DNA and DNA structures interact with inorganic nanomaterials or cells and animals, which should be important for their biological and biomedical applications. In this Account, we intend to provide an overview on many facets of DNA and DNA structures in artificial and living systems, with the focus on their properties and functions at the interfaces of inorganic nanomaterials and biological systems. ssDNA, dsDNA, and DNA nanostructures interact with NMs in different ways. In particular, gold nanoparticles and graphene oxide exhibit strikingly different affinity toward ssDNA and dsDNA. Such binding differences can be coupled with optical properties of NMs. For example, DNA hybridization can effectively modulate the plasmonic and catalytic properties of gold nanoparticles. By exploitation of these interactions, there have been many ways for sensitive transduction of biomolecular recognition for various sensing applications. Alternatively, modulation of the properties of DNA and DNA structures with NMs has led to new tools for genetic analysis including genotyping and haplotyping. Self-assembled DNA nanostructures have emerged as a new type of NMs with pure biomolecules. These nanostructures can be designed in one, two, or three dimensions with various sizes, shapes, and geometries. They also have characteristics of uniform size, precise addressability, excellent water solubility, and biocompatibility. These nanostructures provide a new toolbox for biophysical studies with unparalleled advantages, for example, NMR-based protein structure determination and single-molecule studies. Also importantly, DNA nanostructures have proven highly useful in various applications including biological detection, bioreactors, and nanomedicine. In particular, DNA nanostructures exhibit high cellular permeability, a property that is not available for ssDNA and dsDNA, which is required for their drug delivery applications. DNA and DNA structures can also form hybrids with inorganic NMs. Notably, DNA anchored at the interface of inorganic NMs behaves differently from that at the macroscopic interface. Several types of DNA-NM conjugates have exerted beneficial effects for bioassays and in vitro translation of proteins. Even more interestingly, hybrid nanoconjugates demonstrate distinct properties under the context of biological systems such as cultured cells or animal models. These unprecedented properties not only arouse great interest in studying such interfaces but also open new opportunities for numerous applications in artificial and living systems.
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Affiliation(s)
- Nan Chen
- Division of Physical Biology & Bioimaging Center, Shanghai Sychrotron Radiation Facility (SSRF), CAS Key Laboratory of Microscale Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Jiang Li
- Division of Physical Biology & Bioimaging Center, Shanghai Sychrotron Radiation Facility (SSRF), CAS Key Laboratory of Microscale Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Haiyun Song
- Key
Laboratory of Food Safety Research, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jie Chao
- Division of Physical Biology & Bioimaging Center, Shanghai Sychrotron Radiation Facility (SSRF), CAS Key Laboratory of Microscale Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Qing Huang
- Division of Physical Biology & Bioimaging Center, Shanghai Sychrotron Radiation Facility (SSRF), CAS Key Laboratory of Microscale Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Chunhai Fan
- Division of Physical Biology & Bioimaging Center, Shanghai Sychrotron Radiation Facility (SSRF), CAS Key Laboratory of Microscale Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
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173
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Wang ZG, Ding B. Engineering DNA self-assemblies as templates for functional nanostructures. Acc Chem Res 2014; 47:1654-62. [PMID: 24588320 DOI: 10.1021/ar400305g] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
CONSPECTUS: DNA is a well-known natural molecule that carries genetic information. In recent decades, DNA has been used beyond its genetic role as a building block for the construction of engineering materials. Many strategies, such as tile assembly, scaffolded origami and DNA bricks, have been developed to design and produce 1D, 2D, and 3D architectures with sophisticated morphologies. Moreover, the spatial addressability of DNA nanostructures and sequence-dependent recognition enable functional elements to be precisely positioned and allow for the control of chemical and biochemical processes. The spatial arrangement of heterogeneous components using DNA nanostructures as the templates will aid in the fabrication of functional materials that are difficult to produce using other methods and can address scientific and technical challenges in interdisciplinary research. For example, plasmonic nanoparticles can be assembled into well-defined configurations with high resolution limit while exhibiting desirable collective behaviors, such as near-field enhancement. Conducting metallic or polymer patterns can be synthesized site-specifically on DNA nanostructures to form various controllable geometries, which could be used for electronic nanodevices. Biomolecules can be arranged into organized networks to perform programmable biological functionalities, such as distance-dependent enzyme-cascade activities. DNA nanostructures can carry multiple cytoactive molecules and cell-targeting groups simultaneously to address medical issues such as targeted therapy and combined administration. In this Account, we describe recent advances in the functionalization of DNA nanostructures in different fashions based on our research efforts in nanophotonics, nanoelectronics, and nanomedicine. We show that DNA origami nanostructures can guide the assembly of achiral, spherical, metallic nanoparticles into nature-mimicking chiral geometries through hybridization between complementary DNA strands on the surface of nanoparticles and DNA scaffolds, to generate circular dichroism (CD) response in the visible light region. We also show that DNA nanostructures, on which a HRP-mimicking DNAzyme acts as the catalyst, can direct the site-selective growth of conductive polymer nanomaterials with template configuration-dependent doping behaviors. We demonstrate that DNA origami nanostructures can act as an anticancer-drug carrier, loading drug through intercalation, and can effectively circumvent the drug resistance of cultured cancer cells. Finally, we show a label-free strategy for probing the location and stability of DNA origami nanocarriers in cellular environments by docking turn-off fluorescence dyes in DNA double helices. These functionalizations require further improvement and expansion for realistic applications. We discuss the future opportunities and challenges of DNA based assemblies. We expect that DNA nanostructures as engineering materials will stimulate the development of multidisciplinary and interdisciplinary research.
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Affiliation(s)
- Zhen-Gang Wang
- National Center for NanoScience and Technology, No. 11
BeiYiTiao, ZhongGuanCun, Beijing, 100190 China
| | - Baoquan Ding
- National Center for NanoScience and Technology, No. 11
BeiYiTiao, ZhongGuanCun, Beijing, 100190 China
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174
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Wu TC, Rahman M, Norton ML. From nonfinite to finite 1D arrays of origami tiles. Acc Chem Res 2014; 47:1750-8. [PMID: 24803094 DOI: 10.1021/ar400330y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
CONSPECTUS: DNA based nanotechnology provides a basis for high-resolution fabrication of objects almost without physical size limitations. However, the pathway to large-scale production of large objects is currently unclear. Operationally, one method forward is to use high information content, large building blocks, which can be generated with high yield and reproducibility. Although flat DNA origami naturally invites comparison to pixels in zero, one, and two dimensions and voxels in three dimensions and has provided an excellent mechanism for generating blocks of significant size and complexity and a multitude of shapes, the field is young enough that a single "brick" has not become the standard platform used by the majority of researchers in the field. In this Account, we highlight factors we considered that led to our adoption of a cross-shaped, non-space-filling origami species, designed by Dr. Liu of the Seeman laboratory, as the building block ideal for use in the fabrication of finite one-dimensional arrays. Three approaches that can be employed for uniquely coding origami-origami linkages are presented. Such coding not only provides the energetics for tethering the species but also uniquely designates the relative orientation of the origami building blocks. The strength of the coding approach implemented in our laboratory is demonstrated using examples of oligomers ranging from finite multimers composed of four, six, and eight origami structures to semi-infinite polymers (100mers). Two approaches to finite array design and the series of assembly steps that each requires are discussed. The process of AFM observation for array characterization is presented as a critical case study. For these soft species, the array images do not simply present the solution phase geometry projected onto a two-dimensional surface. There are additional perturbations associated with fluidic forces associated with sample preparation. At this time, reconstruction of the "true" or average solution structures for blocks is more readily achieved using computer models than using direct imaging methods. The development of scalable 1D-origami arrays composed of uniquely addressable components is a logical, if not necessary, step in the evolution of higher order fully addressable structures. Our research into the fabrication of arrays has led us to generate a listing of several important areas of future endeavor. Of high importance is the re-enforcement of the mechanical properties of the building blocks and the organization of multiple arrays on a surface of technological importance. While addressing this short list of barriers to progress will prove challenging, coherent development along each of these lines of inquiry will accelerate the appearance of commercial scale molecular manufacturing.
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Affiliation(s)
- Tsai Chin Wu
- Department of Chemistry, Marshall University, 1 John Marshall Drive, Huntingon, West Virginia 25755, United States
| | - Masudur Rahman
- Department of Chemistry, Marshall University, 1 John Marshall Drive, Huntingon, West Virginia 25755, United States
| | - Michael L. Norton
- Department of Chemistry, Marshall University, 1 John Marshall Drive, Huntingon, West Virginia 25755, United States
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175
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Koirala D, Shrestha P, Emura T, Hidaka K, Mandal S, Endo M, Sugiyama H, Mao H. Single-Molecule Mechanochemical Sensing Using DNA Origami Nanostructures. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201404043] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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176
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Koirala D, Shrestha P, Emura T, Hidaka K, Mandal S, Endo M, Sugiyama H, Mao H. Single-Molecule Mechanochemical Sensing Using DNA Origami Nanostructures. Angew Chem Int Ed Engl 2014; 53:8137-41. [DOI: 10.1002/anie.201404043] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2014] [Indexed: 01/01/2023]
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177
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178
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Aghebat Rafat A, Pirzer T, Scheible MB, Kostina A, Simmel FC. Surface-Assisted Large-Scale Ordering of DNA Origami Tiles. Angew Chem Int Ed Engl 2014; 53:7665-8. [DOI: 10.1002/anie.201403965] [Citation(s) in RCA: 130] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Indexed: 11/09/2022]
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179
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Gates EP, Dearden AM, Woolley AT. DNA‐templated lithography and nanofabrication for the fabrication of nanoscale electronic circuitry. Crit Rev Anal Chem 2014; 44:354-70. [DOI: 10.1080/10408347.2014.910636] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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180
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Discovering anomalous hybridization kinetics on DNA nanostructures using single-molecule fluorescence microscopy. Methods 2014; 67:177-84. [DOI: 10.1016/j.ymeth.2014.02.032] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 02/04/2014] [Accepted: 02/21/2014] [Indexed: 11/21/2022] Open
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181
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Pei H, Zuo X, Zhu D, Huang Q, Fan C. Functional DNA nanostructures for theranostic applications. Acc Chem Res 2014; 47:550-9. [PMID: 24380626 DOI: 10.1021/ar400195t] [Citation(s) in RCA: 301] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
There has been tremendous interest in constructing nanostructures by exploiting the unparalleled ability of DNA molecules in self-assembly. We have seen the appearance of many fantastic, "art-like" DNA nanostructures in one, two, or three dimensions during the last two decades. More recently, much attention has been directed to the use of these elegant nanoobjects for applications in a wide range of areas. Among them, diagnosis and therapy (i.e., theranostics) are of particular interest given the biological nature of DNA. One of the major barricades for the biosensor design lies in the restricted target accessibility at the solid-water interface. DNA nanotechnology provides a convenient approach to well control the biomolecule-confined surface to increase the ability of molecular recognition at the biosensing interface. For example, tetrahedral DNA nanostructures with thiol modifications can be self-assembled at the gold surface with high reproducibility. Since DNA tetrahedra are highly rigid and well-defined structures with atomic precision and versatile functionality, they provide scaffolds for anchoring of a variety of biomolecular probes (DNA, aptamers, peptides, and proteins) for biosensing. Significantly, this DNA nanostructure-based biosensing platform greatly increases target accessibility and improves the sensitivity for various types of molecular targets (DNA, RNA, proteins, and small molecules) by several orders of magnitude. In an alternative approach, DNA nanostructures provide a framework for the development of dynamic nanosensors that can function inside the cell. DNA tetrahedra are found to be facilely cell permeable and can sense and image specific molecules in cells. More importantly, these DNA nanostructures can be efficient drug delivery nanocarriers. Since they are DNA molecules by themselves, they have shown excellent cellular biocompatibility with minimal cytotoxicity. As an example, DNA tetrahedra tailored with CpG oligonucleotide drugs have shown greatly improved immunostimulatory effects that makes them a highly promising nanomedicine. By taking them together, we believe these functionalized DNA nanostructures can be a type of intelligent theranostic nanodevice for simultaneous sensing, diagnosis, and therapy inside the cell.
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Affiliation(s)
- Hao Pei
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Microscale Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Xiaolei Zuo
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Microscale Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Dan Zhu
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Microscale Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Qing Huang
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Microscale Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Chunhai Fan
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Microscale Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
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182
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Pei H, Zuo X, Zhu D, Huang Q, Fan C. Functional DNA nanostructures for theranostic applications. Acc Chem Res 2014; 47:550-559. [PMID: 24380626 DOI: 10.1002/9781118998922.ch4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
There has been tremendous interest in constructing nanostructures by exploiting the unparalleled ability of DNA molecules in self-assembly. We have seen the appearance of many fantastic, "art-like" DNA nanostructures in one, two, or three dimensions during the last two decades. More recently, much attention has been directed to the use of these elegant nanoobjects for applications in a wide range of areas. Among them, diagnosis and therapy (i.e., theranostics) are of particular interest given the biological nature of DNA. One of the major barricades for the biosensor design lies in the restricted target accessibility at the solid-water interface. DNA nanotechnology provides a convenient approach to well control the biomolecule-confined surface to increase the ability of molecular recognition at the biosensing interface. For example, tetrahedral DNA nanostructures with thiol modifications can be self-assembled at the gold surface with high reproducibility. Since DNA tetrahedra are highly rigid and well-defined structures with atomic precision and versatile functionality, they provide scaffolds for anchoring of a variety of biomolecular probes (DNA, aptamers, peptides, and proteins) for biosensing. Significantly, this DNA nanostructure-based biosensing platform greatly increases target accessibility and improves the sensitivity for various types of molecular targets (DNA, RNA, proteins, and small molecules) by several orders of magnitude. In an alternative approach, DNA nanostructures provide a framework for the development of dynamic nanosensors that can function inside the cell. DNA tetrahedra are found to be facilely cell permeable and can sense and image specific molecules in cells. More importantly, these DNA nanostructures can be efficient drug delivery nanocarriers. Since they are DNA molecules by themselves, they have shown excellent cellular biocompatibility with minimal cytotoxicity. As an example, DNA tetrahedra tailored with CpG oligonucleotide drugs have shown greatly improved immunostimulatory effects that makes them a highly promising nanomedicine. By taking them together, we believe these functionalized DNA nanostructures can be a type of intelligent theranostic nanodevice for simultaneous sensing, diagnosis, and therapy inside the cell.
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Affiliation(s)
- Hao Pei
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Microscale Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
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183
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Digital imprinting of RNA recognition and processing on a self-assembled nucleic acid matrix. Sci Rep 2014; 3:2550. [PMID: 23989631 PMCID: PMC3757352 DOI: 10.1038/srep02550] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Accepted: 08/08/2013] [Indexed: 11/08/2022] Open
Abstract
The accelerating progress of research in nanomedicine and nanobiotechnology has included initiatives to develop highly-sensitive, high-throughput methods to detect biomarkers at the single-cell level. Current sensing approaches, however, typically involve integrative instrumentation that necessarily must balance sensitivity with rapidity in optimizing biomarker detection quality. We show here that laterally-confined, self-assembled monolayers of a short, double-stranded(ds)[RNA-DNA] chimera enable permanent digital detection of dsRNA-specific inputs. The action of ribonuclease III and the binding of an inactive, dsRNA-binding mutant can be permanently recorded by the input-responsive action of a restriction endonuclease that cleaves an ancillary reporter site within the dsDNA segment. The resulting irreversible height change of the arrayed ds[RNA-DNA], as measured by atomic force microscopy, provides a distinct digital output for each dsRNA-specific input. These findings provide the basis for developing imprinting-based bio-nanosensors, and reveal the versatility of AFM as a tool for characterizing the behaviour of highly-crowded biomolecules at the nanoscale.
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184
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Wang D, Fu Y, Yan J, Zhao B, Dai B, Chao J, Liu H, He D, Zhang Y, Fan C, Song S. Molecular Logic Gates on DNA Origami Nanostructures for MicroRNA Diagnostics. Anal Chem 2014; 86:1932-6. [DOI: 10.1021/ac403661z] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Dongfang Wang
- Laboratory
of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Yanming Fu
- Laboratory
of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Juan Yan
- Laboratory
of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- National Engineering Research Center for Nanotechnology, Shanghai 200241, China
| | - Bin Zhao
- Laboratory
of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Bin Dai
- Laboratory
of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Jie Chao
- Laboratory
of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Huajie Liu
- Laboratory
of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Dannong He
- National Engineering Research Center for Nanotechnology, Shanghai 200241, China
| | - Yi Zhang
- Laboratory
of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Chunhai Fan
- Laboratory
of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Shiping Song
- Laboratory
of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
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185
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Rajendran A, Endo M, Hidaka K, Thao Tran PL, Teulade-Fichou MP, Mergny JL, Sugiyama H. G-quadruplex-binding ligand-induced DNA synapsis inside a DNA origami frame. RSC Adv 2014. [DOI: 10.1039/c3ra45676e] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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186
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de Vries JW, Zhang F, Herrmann A. Drug delivery systems based on nucleic acid nanostructures. J Control Release 2013; 172:467-83. [DOI: 10.1016/j.jconrel.2013.05.022] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Revised: 05/23/2013] [Accepted: 05/24/2013] [Indexed: 01/26/2023]
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187
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Wu C, Han D, Chen T, Peng L, Zhu G, You M, Qiu L, Sefah K, Zhang X, Tan W. Building a multifunctional aptamer-based DNA nanoassembly for targeted cancer therapy. J Am Chem Soc 2013; 135:18644-50. [PMID: 24245521 DOI: 10.1021/ja4094617] [Citation(s) in RCA: 193] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The ability to self-assemble one-dimensional DNA building blocks into two- and three-dimensional nanostructures via DNA/RNA nanotechnology has led to broad applications in bioimaging, basic biological mechanism studies, disease diagnosis, and drug delivery. However, the cellular uptake of most nucleic acid nanostructures is dependent on passive delivery or the enhanced permeability and retention effect, which may not be suitable for certain types of cancers, especially for treatment in vivo. To meet this need, we have constructed a multifunctional aptamer-based DNA nanoassembly (AptNA) for targeted cancer therapy. In particular, we first designed various Y-shaped functional DNA domains through predesigned base pair hybridization, including targeting aptamers, intercalated anticancer drugs, and therapeutic antisense oligonucleotides. Then these functional DNA domains were linked to an X-shaped DNA core connector, termed a building unit, through the complementary sequences in the arms of functional domains and connector. Finally, hundreds (~100-200) of these basic building units with 5'-modification of acrydite groups were further photo-cross-linked into a multifunctional and programmable aptamer-based nanoassembly structure able to take advantage of facile modular design and assembly, high programmability, excellent biostability and biocompatibility, as well as selective recognition and transportation. With these properties, AptNAs were demonstrated to have specific cytotoxic effect against leukemia cells. Moreover, the incorporation of therapeutic antisense oligonucleotides resulted in the inhibition of P-gp expression (a drug efflux pump to increase excretion of anticancer drugs) as well as a decrease in drug resistance. Therefore, these multifunctional and programmable aptamer-based DNA nanoassemblies show promise as candidates for targeted drug delivery and cancer therapy.
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Affiliation(s)
- Cuichen Wu
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at Bio/Nano Interface, Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida , Gainesville, Florida 32611-7200, United States
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188
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Zhang C, Ma J, Yang J, Liu S, Xu J. Binding Assistance Triggering Attachments of Hairpin DNA onto Gold Nanoparticles. Anal Chem 2013; 85:11973-8. [DOI: 10.1021/ac402908y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Cheng Zhang
- Institute of Software, School of Electronics Engineering
and Computer Science, Peking University, Key Laboratory of High Confidence Software Technologies, Ministry of Education, Beijing, China
| | - Jingjing Ma
- Institute of Software, School of Electronics Engineering
and Computer Science, Peking University, Key Laboratory of High Confidence Software Technologies, Ministry of Education, Beijing, China
| | - Jing Yang
- School of Control and Computer Engineering, North China Electric Power University, Beijing, 102206, China
| | - Shi Liu
- School of Control and Computer Engineering, North China Electric Power University, Beijing, 102206, China
| | - Jin Xu
- Institute of Software, School of Electronics Engineering
and Computer Science, Peking University, Key Laboratory of High Confidence Software Technologies, Ministry of Education, Beijing, China
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189
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Chen Z, Lan X, Wang Q. DNA origami directed large-scale fabrication of nanostructures resembling room temperature single-electron transistors. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2013; 9:3567-3571. [PMID: 23813856 DOI: 10.1002/smll.201300640] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 03/25/2013] [Indexed: 06/02/2023]
Abstract
Room temperature single-electron transistor core nanostructures are fabricated on a large scale with DNA origami as a template with an unprecedented yield. The accuracy of DNA origami enables precise positioning of a Coulomb island in the center of a 10 nm gap between the source and the drain electrodes, which can not be realized by using state-of-the-art nanofabrication techniques.
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Affiliation(s)
- Zhong Chen
- Suzhou Key Laboratory of Nanomedical Characterization, Division of Nanobiomedicine and i-Lab, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, PR China
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190
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Pastré D, Joshi V, Curmi PA, Hamon L. Detection of single DNA molecule hybridization on a surface by atomic force microscopy. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2013; 9:3630-3638. [PMID: 23674511 DOI: 10.1002/smll.201300546] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Indexed: 06/02/2023]
Abstract
Improving the detection of DNA hybridization is a critical issue for several challenging applications encountered in microarray and biosensor domains. Herein, it is demonstrated that hybridization between complementary single-stranded DNA (ssDNA) molecules loosely adsorbed on a mica surface can be achieved thanks to fine-tuning of the composition of the hybridization buffer. Single-molecule DNA hybridization occurs in only a few minutes upon encounters of freely diffusing complementary strands on the mica surface. Interestingly, the specific hybridization between complementary ssDNA is not altered in the presence of large amounts of nonrelated DNA. The detection of single-molecule DNA hybridization events is performed by measuring the contour length of DNA in atomic force microscopy images. Besides the advantage provided by facilitated diffusion, which promotes hybridization between probes and targets on mica, the present approach also allows the detection of single isolated DNA duplexes and thus requires a very low amount of both probe and target molecules.
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Affiliation(s)
- David Pastré
- Inserm U829, Laboratoire Structure-Activité des, Biomolécules Normales et Pathologiques, Université d'Evry-Val d'Essonne, Evry 91025, France
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191
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Zhang C, Wu L, Yang J, Liu S, Xu J. A molecular logical switching beacon controlled by thiolated DNA signals. Chem Commun (Camb) 2013; 49:11308-10. [PMID: 24158378 DOI: 10.1039/c3cc46743k] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A logical switching MB is established, with an "ON/OFF" switching function. In this study, thiolated DNA can participate as a switching controller to regulate the fluorescent increments of other DNA input signals. Assisted by gold nanoparticles and DNA branch migration, one and two-switch systems have been achieved.
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Affiliation(s)
- Cheng Zhang
- Institute of Software, School of Electronics Engineering and Computer Science, Peking University, Key laboratory of High Confidence Software Technologies, Ministry of Education, Beijing, China.
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192
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Rashidian M, Kumarapperuma SC, Gabrielse K, Fegan A, Wagner CR, Distefano MD. Simultaneous dual protein labeling using a triorthogonal reagent. J Am Chem Soc 2013; 135:16388-96. [PMID: 24134212 DOI: 10.1021/ja403813b] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Construction of heterofunctional proteins is a rapidly emerging area of biotherapeutics. Combining a protein with other moieties, such as a targeting element, a toxic protein or small molecule, and a fluorophore or polyethylene glycol (PEG) group, can improve the specificity, functionality, potency, and pharmacokinetic profile of a protein. Protein farnesyl transferase (PFTase) is able to site-specifically and quantitatively prenylate proteins containing a C-terminal CaaX-box amino acid sequence with various modified isoprenoids. Here, we describe the design, synthesis, and application of a triorthogonal reagent, 1, that can be used to site-specifically incorporate an alkyne and aldehyde group simultaneously into a protein. To illustrate the capabilities of this approach, a protein was enzymatically modified with compound 1 followed by oxime ligation and click reaction to simultaneously incorporate an azido-tetramethylrhodamine (TAMRA) fluorophore and an aminooxy-PEG moiety. This was performed with both a model protein [green fluorescent protein (GFP)] as well as a therapeutically useful protein [ciliary neurotrophic factor (CNTF)]. Next, a protein was enzymatically modified with compound 1 followed by coupling to an azido-bis-methotrexate dimerizer and aminooxy-TAMRA. Incubation of that construct with a dihydrofolate reductase (DHFR)-DHFR-anti-CD3 fusion protein resulted in the self-assembly of nanoring structures that were endocytosed into T-leukemia cells and visualized therein. These results highlight how complex multifunctional protein assemblies can be prepared using this facile triorthogonal approach.
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Affiliation(s)
- Mohammad Rashidian
- Department of Chemistry, and §Department of Medicinal Chemistry, University of Minnesota , Minneapolis, Minnesota 55455, United States
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193
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Qiu M, Khisamutdinov E, Zhao Z, Pan C, Choi JW, Leontis NB, Guo P. RNA nanotechnology for computer design and in vivo computation. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2013; 371:20120310. [PMID: 24000362 PMCID: PMC3758167 DOI: 10.1098/rsta.2012.0310] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Molecular-scale computing has been explored since 1989 owing to the foreseeable limitation of Moore's law for silicon-based computation devices. With the potential of massive parallelism, low energy consumption and capability of working in vivo, molecular-scale computing promises a new computational paradigm. Inspired by the concepts from the electronic computer, DNA computing has realized basic Boolean functions and has progressed into multi-layered circuits. Recently, RNA nanotechnology has emerged as an alternative approach. Owing to the newly discovered thermodynamic stability of a special RNA motif (Shu et al. 2011 Nat. Nanotechnol. 6, 658-667 (doi:10.1038/nnano.2011.105)), RNA nanoparticles are emerging as another promising medium for nanodevice and nanomedicine as well as molecular-scale computing. Like DNA, RNA sequences can be designed to form desired secondary structures in a straightforward manner, but RNA is structurally more versatile and more thermodynamically stable owing to its non-canonical base-pairing, tertiary interactions and base-stacking property. A 90-nucleotide RNA can exhibit 4⁹⁰ nanostructures, and its loops and tertiary architecture can serve as a mounting dovetail that eliminates the need for external linking dowels. Its enzymatic and fluorogenic activity creates diversity in computational design. Varieties of small RNA can work cooperatively, synergistically or antagonistically to carry out computational logic circuits. The riboswitch and enzymatic ribozyme activities and its special in vivo attributes offer a great potential for in vivo computation. Unique features in transcription, termination, self-assembly, self-processing and acid resistance enable in vivo production of RNA nanoparticles that harbour various regulators for intracellular manipulation. With all these advantages, RNA computation is promising, but it is still in its infancy. Many challenges still exist. Collaborations between RNA nanotechnologists and computer scientists are necessary to advance this nascent technology.
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Affiliation(s)
- Meikang Qiu
- Department of Computer Engineering, San Jose State University, San Jose, CA 95192, USA
| | - Emil Khisamutdinov
- Department of Pharmaceutical Science, University of Kentucky, Lexington, KY 40506, USA
| | - Zhengyi Zhao
- Department of Pharmaceutical Science, University of Kentucky, Lexington, KY 40506, USA
| | - Cheryl Pan
- Department of Electrical and Computer Engineering, University of Kentucky, Lexington, KY 40506, USA
| | - Jeong-Woo Choi
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul 121-742, Korea
| | - Neocles B. Leontis
- Department of Chemistry, Bowling Green State University, Bowling Green, OH 43403, USA
| | - Peixuan Guo
- Department of Pharmaceutical Science, University of Kentucky, Lexington, KY 40506, USA
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194
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Li J, Fan C, Pei H, Shi J, Huang Q. Smart drug delivery nanocarriers with self-assembled DNA nanostructures. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2013; 25:4386-96. [PMID: 23765613 DOI: 10.1002/adma.201300875] [Citation(s) in RCA: 308] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 04/15/2013] [Indexed: 05/23/2023]
Abstract
Self-assembled DNA nanostructures have emerged as a type of nano-biomaterials with precise structures, versatile functions and numerous applications. One particularly promising application of these DNA nanostructures is to develop universal nanocarriers for smart and targeted drug delivery. DNA is the genetic material in nature, and inherently biocompatible. Nevertheless, cell membranes are barely permeable to naked DNA molecules, either single- or double- stranded; transport across the cell membrane is only possible with the assistance of transfection agents. Interestingly, recent studies revealed that many DNA nanostructures could readily go into cells with high cell uptake efficiency. In this Progress Report, we will review recent advances on using various DNA nanostructures, e.g., DNA nanotubes, DNA tetrahedra, and DNA origami nanorobot, as drug delivery nanocarriers, and demonstrate several examples aiming at therapeutic applications with CpG-based immunostimulatory and siRNA-based gene silencing oligonucleotides.
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Affiliation(s)
- Jiang Li
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China
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195
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Accurate quantification of microRNA via single strand displacement reaction on DNA origami motif. PLoS One 2013; 8:e69856. [PMID: 23990889 PMCID: PMC3749204 DOI: 10.1371/journal.pone.0069856] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Accepted: 06/12/2013] [Indexed: 11/19/2022] Open
Abstract
DNA origami is an emerging technology that assembles hundreds of staple strands and one single-strand DNA into certain nanopattern. It has been widely used in various fields including detection of biological molecules such as DNA, RNA and proteins. MicroRNAs (miRNAs) play important roles in post-transcriptional gene repression as well as many other biological processes such as cell growth and differentiation. Alterations of miRNAs' expression contribute to many human diseases. However, it is still a challenge to quantitatively detect miRNAs by origami technology. In this study, we developed a novel approach based on streptavidin and quantum dots binding complex (STV-QDs) labeled single strand displacement reaction on DNA origami to quantitatively detect the concentration of miRNAs. We illustrated a linear relationship between the concentration of an exemplary miRNA as miRNA-133 and the STV-QDs hybridization efficiency; the results demonstrated that it is an accurate nano-scale miRNA quantifier motif. In addition, both symmetrical rectangular motif and asymmetrical China-map motif were tested. With significant linearity in both motifs, our experiments suggested that DNA Origami motif with arbitrary shape can be utilized in this method. Since this DNA origami-based method we developed owns the unique advantages of simple, time-and-material-saving, potentially multi-targets testing in one motif and relatively accurate for certain impurity samples as counted directly by atomic force microscopy rather than fluorescence signal detection, it may be widely used in quantification of miRNAs.
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196
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Lan X, Chen Z, Dai G, Lu X, Ni W, Wang Q. Bifacial DNA Origami-Directed Discrete, Three-Dimensional, Anisotropic Plasmonic Nanoarchitectures with Tailored Optical Chirality. J Am Chem Soc 2013; 135:11441-4. [DOI: 10.1021/ja404354c] [Citation(s) in RCA: 187] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Xiang Lan
- Suzhou Key
Laboratory of Nanobiomedical Characterization, Division of Nanobiomedicine
and i-Lab, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
| | - Zhong Chen
- Suzhou Key
Laboratory of Nanobiomedical Characterization, Division of Nanobiomedicine
and i-Lab, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
| | - Gaole Dai
- Suzhou Key
Laboratory of Nanobiomedical Characterization, Division of Nanobiomedicine
and i-Lab, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
| | - Xuxing Lu
- Suzhou Key
Laboratory of Nanobiomedical Characterization, Division of Nanobiomedicine
and i-Lab, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
| | - Weihai Ni
- Suzhou Key
Laboratory of Nanobiomedical Characterization, Division of Nanobiomedicine
and i-Lab, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
| | - Qiangbin Wang
- Suzhou Key
Laboratory of Nanobiomedical Characterization, Division of Nanobiomedicine
and i-Lab, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
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197
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Wang ZG, Song C, Ding B. Functional DNA nanostructures for photonic and biomedical applications. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2013; 9:2210-2222. [PMID: 23733711 DOI: 10.1002/smll.201300141] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Indexed: 06/02/2023]
Abstract
DNA nanostructures, especially DNA origami, receive close interest because of the programmable control over their shape and size, precise spatial addressability, easy and high-yield preparation, mechanical flexibility, and biocompatibility. They have been used to organize a variety of nanoscale elements for specific functions, resulting in unprecedented improvements in the field of nanophotonics and nanomedical research. In this review, the discussion focuses on the employment of DNA nanostructures for the precise organization of noble metal nanoparticles to build interesting plasmonic nanoarchitectures, for the fabrication of visualized sensors and for targeted drug delivery. The effects offered by DNA nanostructures are highlighted in the areas of nanoantennas, collective plasmonic behaviors, single-molecule analysis, and cancer-cell targeting or killing. Finally, the challenges in the field of DNA nanotechnology for realistic application are discussed and insights for future directions are provided.
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Affiliation(s)
- Zhen-Gang Wang
- National Center for Nanoscience and Technology, Beijing 100190, PR China
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198
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Hartman MR, Yang D, Tran TNN, Lee K, Kahn JS, Kiatwuthinon P, Yancey KG, Trotsenko O, Minko S, Luo D. Thermostable branched DNA nanostructures as modular primers for polymerase chain reaction. Angew Chem Int Ed Engl 2013; 52:8699-702. [PMID: 23825018 DOI: 10.1002/anie.201302175] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Indexed: 01/12/2023]
Affiliation(s)
- Mark R Hartman
- Department of Biological & Environmental Engineering, Cornell University, Ithaca, NY 14853, USA
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199
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Hartman MR, Yang D, Tran TNN, Lee K, Kahn JS, Kiatwuthinon P, Yancey KG, Trotsenko O, Minko S, Luo D. Thermostable Branched DNA Nanostructures as Modular Primers for Polymerase Chain Reaction. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201302175] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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200
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Muscat RA, Strauss K, Ceze L, Seelig G. DNA-based molecular architecture with spatially localized components. ACTA ACUST UNITED AC 2013. [DOI: 10.1145/2508148.2485938] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Performing computation inside living cells offers life-changing applications, from improved medical diagnostics to better cancer therapy to intelligent drugs. Due to its bio-compatibility and ease of engineering, one promising approach for performing in-vivo computation is DNA strand displacement. This paper introduces computer architects to DNA strand displacement "circuits", discusses associated architectural challenges, and proposes a new organization that provides practical composability. In particular, prior approaches rely mostly on stochastic interaction of freely diffusing components. This paper proposes practical
spatial
isolation of components, leading to more easily designed DNA-based circuits. DNA nanotechnology is currently at a turning point, with many proposed applications being realized [20, 9]. We believe that it is time for the computer architecture community to take notice and contribute.
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